Just an FYI.
Arduino has now released Arduino 1.6.0 which is the first non beta Arduino IDE to support the Due/... This release all replaces the Arduino 1.0.x releases which will sortof go into an archive state.
So with this release the directory/library structures should be pretty will fixed. So it would be great if Intel migrated to this release.
Also it may be wishful thinking, but it would be even better if they did it, sort of like how PJRC does with the Teensy's where he has an installer application which installs your hardware specific stuff into the appropriate locations on a users install. i.e - I would really like it if I could have just one copy of the Arduino IDE on my machines, instead of my 4-5 versions I currently have.
FYI - Yesterday while using the current arduino (arduino.cc) version which is 1.6.3, and I went to Tools/Board menu and choose the Boards Manager, I saw two new options for installs (Edison and Galileo), so I instructed it to download these, which it did. .
Note: The new Arduino builds by default only download AVR boards, for other boards include Due, you need to use the boards manager to download the support for them. Note: the new system does not install the hardware files at the same location (as a sub-tree of the install), but instead at some specific location: In Windows case on my machine: C:\Users\Kurt\AppData\Roaming\Arduino15
Personally I am not sure about storing all of this under the per user app data, but that is more a discussion for Arduino.
More details about this up at: https://github.com/arduino/Arduino/wiki/Boards-Manager-FAQ
Side note, there are also changes in how library files are located that changed in some of the more recent Arduino builds. More details about the new library manager up at: Library Manager FAQ · arduino/Arduino Wiki · GitHub
I have not fully tried this out, other than to verify that I could compile a program. I also used winmerge to see what all has changed from this set of cores to the current one from the Intel Site. Source code wise, I only see a change in TTYUART.cpp, which at first glance looks like some change on handling Serial2...